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need command to match snps - Printable Version +- The GenArchivist Forum (https://genarchivist.net) +-- Forum: Human Personal & Genealogical Genetics (https://genarchivist.net/forumdisplay.php?fid=1) +--- Forum: Inquiries Corner (https://genarchivist.net/forumdisplay.php?fid=20) +--- Thread: need command to match snps (/showthread.php?tid=1350) |
need command to match snps - Genetics189291 - 12-24-2024 I want to match the snps (rsid) from a file I have to my dataset so that it only matches those snps. I've tried several commands and it's just not doing it RE: need command to match snps - AimSmall - 12-24-2024 (12-24-2024, 10:31 PM)Genetics189291 Wrote: I want to match the snps (rsid) from a file I have to my dataset so that it only matches those snps. I've tried several commands and it's just not doing it plink(version number) --bfile "dataset" --keep extractlist --make-bed --out "your sample" RE: need command to match snps - Genetics189291 - 12-24-2024 (12-24-2024, 10:35 PM)AimSmall Wrote:(12-24-2024, 10:31 PM)Genetics189291 Wrote: I want to match the snps (rsid) from a file I have to my dataset so that it only matches those snps. I've tried several commands and it's just not doing it I should have mentioned it's a .txt file it's formatted in this way rs6668 rs2134532 etc when I use that command it tells me line 1 of keep file has fewer tokens then expected RE: need command to match snps - AimSmall - 12-24-2024 My bad.... keep is for samples Use --snps Think you can put a filename after the --snps Code: Multiple ranges RE: need command to match snps - AimSmall - 12-24-2024 plink --bfile data --extract snps.txt --recodeA RE: need command to match snps - Genetics189291 - 12-24-2024 (12-24-2024, 10:53 PM)AimSmall Wrote: My bad.... keep is for samples I tried this but it didn't seem to work I tried the command below which also didn't seem to work, I can go through it one by one and filter it but it would take a long time to do RE: need command to match snps - AimSmall - 12-25-2024 Post your snp restriction file RE: need command to match snps - nomad01 - 12-25-2024 do you mean the " --extract snp.txt " command? RE: need command to match snps - Genetics189291 - 12-25-2024 (12-25-2024, 12:11 AM)AimSmall Wrote: Post your snp restriction file will do RE: need command to match snps - Genetics189291 - 12-25-2024 (12-25-2024, 09:30 AM)nomad01 Wrote: do you mean the " --extract snp.txt " command? I tried this and it seemed not to work, I checked the files and it didn't execute the command, I also tried awk but no luck RE: need command to match snps - nomad01 - 12-25-2024 (12-25-2024, 12:55 PM)Genetics189291 Wrote:(12-25-2024, 09:30 AM)nomad01 Wrote: do you mean the " --extract snp.txt " command? it should be working, bed/bim/fam, plink2.exe and snp.txt should all be in the same folder RE: need command to match snps - Genetics189291 - 12-25-2024 (12-25-2024, 01:30 PM)nomad01 Wrote:(12-25-2024, 12:55 PM)Genetics189291 Wrote:(12-25-2024, 09:30 AM)nomad01 Wrote: do you mean the " --extract snp.txt " command? I’m gonna try when I get home |